23andMe raises $50M, cuts price to $99, sets goal of 1M genotyped customers

This is the precise reason for the "individual mandate" in Obamacare. The two provisions only work in combination.

I did a news search to see what researchers are saying recently about the data analyzed by 23andMe. One news article led me to a company blog post by a bioinformatics researcher, Gabe Rudy, "GATK is a Research Tool. Clinics Beware"

http://blog.goldenhelix.com/?p=1534

in which he applied his own industry knowledge to his updated 23andMe report. His conclusions suggest that the product needs much more work:

"I promptly sent an email off to 23andMe’s exome team letting them know about what is clearly a bug in the GATK variant caller. They confirmed it was a bug that went away after updating to a newer release. I talked to 23andMe’s bioinformatician behind the report face-to-face a bit at this year’s ASHG conference, and it sounds like it was most likely a bug in the tool’s multi-sample variant calling mode as this phantom insertion was a real insertion in one of the other samples."

. . . .

"But because GATK has been used so prolifically in publications and is backed by the Broad Institute, it can be viewed as a 'safe' choice. As small labs and clinical centers around the world are starting to set up their DNA-seq pipelines for gene panel and exome sequencing, they may choose GATK with the assumption that the output doesn’t need to be validated.

"And that would be a mistake.

"GATK is as susceptible to bugs as much as any complex software. Their new mixed licensing model (free for academic, fee for commercial) is intended to add more dedicated support resources to the team. I suggest they think about adding dedicated testers as well."

So for those of us following along at home, the crucial idea is that most of the "information" that 23andMe provides paying clients has not been validated. Not only has it not been validated as to correctness of the genome analysis software (the industry scientist's observation), it has even less been validated as a clue to clinically significant disease risk for the majority of diseases that afflict people in developed countries. Pay your money for the service at the new lower price if you like, but prepared to see your personal genome results repackaged and reinterpreted for years to come before you learn anything from them that will help you improve your health.

Interesting article, although I think the author incorrectly blames the software tool rather than 23andMe.

The GATK is a research tool in active development. "Clinics beware" makes little sense because it's not like there is any real alternative (aside from other research tools). This is new territory for everyone. It almost strikes me in the same way as if someone were to say, "Users beware: Linux is a research tool". Whether or not it is a research tool doesn't change that misuse of the tool will lead to poor results.

It's been a little over a year since I last directly used the GATK's caller, but at that time indel calling (the thing that produced this blogger's error) was experimental and clearly labeled as such in loud capital letters.

Also, the GATK does not make one use insane parameters such as allowing variant calls supported by 0 reads; that's the choice of the person running the software...

Thanks very much for your reply.

This is new territory for everyone.

I have developed a habit of liberally upvoting most of your comments on threads related to biology, as I consistently learn from them and see you taking the time and effort to correct popular misconceptions as you participate here. So knowing that I'm asking someone who'll give me a straight answer, I wonder if you could comment specifically on my statement above

"So for those of us following along at home, the crucial idea is that most of the 'information' that 23andMe provides paying clients has not been validated. Not only has it not been validated as to correctness of the genome analysis software (the industry scientist's observation), it has even less been validated as a clue to clinically significant disease risk for the majority of diseases that afflict people in developed countries. Pay your money for the service at the new lower price if you like, but prepared to see your personal genome results repackaged and reinterpreted for years to come before you learn anything from them that will help you improve your health."

I'm heartily in agreement with the idea of doing fundamental research on the human genome and gathering large datasets to analyze to look for genetic clues to human health and disease. I participate each week during the school year in the University of Minnesota "journal club" on behavior genetics, in which a group of scientists (mostly psychologists, but a few mathematicians and economists) who investigate genetic influences on human behavior meet to discuss the latest papers on new research. The overwhelming impression I get is that commercial businesses like 23andMe certainly mean well, and are trying to make available new gene analysis tools to a broader public. But that they are running ahead of their ability, based on current science, to deliver actionable information to the clients who pay for their services. There is still an astounding lack of replicability and of large effect sizes in almost any genome study related to common human diseases or to socially meaningful human behaviors. Much more research needs to be done.

Why is it so expensive to ship internationally?